Nature Methods Contents: September 2014 Volume 11 pp 875 - 972

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Advertisement Prepare Large-Scale Epigenetics Libraries with EpiGnome™ Construct large-scale WGBS libraries with the new 24- and 96-reaction EpiGnome Methyl-Seq kits. Post-bisulfite conversion library construction preserves more DNA fragments, expanding the sample types that can be sequenced on Illumina® HiSeq Systems. Capture robust methylation data on medically relevant genes and high-interest promoters from small samples (50-100 ng). TABLE OF CONTENTS September 2014 Volume 11, Issue 9 In This Issue Editorials This Month Correspondence Research Highlights Commentaries Technology Feature News and Views Brief Communications Articles Corrigenda Addendum Application Notes Advertisement   Powerful reasons to choose Reichert Surface Plasmon Resonance (SPR) systems for your lab Reichert SPR systems beat the competition! Unparalleled performance. Unmatched sensitivity. Robust off-the-shelf fluidics. Low operating costs. Outstanding support for your applications from expert scientists. No better value. Compare for yourself. ReichertSPR.com/advantage  Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nature has once again been ranked the N0.1 weekly science journal with an Impact Factor of 42.351*. To celebrate we are offering you the opportunity to subscribe at an exclusive limited time offer of only $42, £42 or €42. This is a limited time offer - so don't miss out and subscribe today! *2013 Journal Citation Reports® (Thomson Reuters, 2014)     In This Issue Top InThisIssue    Editorials Top The measure of reproducibility   p875 doi:10.1038/nmeth.3096 A clear idea of the performance—the strengths but also the limits—of biological research methods is critical for generating reliable data that others are able to reproduce. Change at Nature Methods   p875 doi:10.1038/nmeth.3097 We announce a change in leadership at Nature Methods and wish Daniel Evanko, our departing chief editor and the new head of editorial services at Nature Publishing Group, every success. This Month Top The Author File: Richard Neutze   p877 Vivien Marx doi:10.1038/nmeth.3074 Proteins 'breathe' in an ultrafast way that can be captured with XFELs. Points of Significance: Replication   pp879 - 880 Paul Blainey, Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.3091 Quality is often more important than quantity. Correspondence Top Light-sheet functional imaging in fictively behaving zebrafish   pp883 - 884 Nikita Vladimirov, Yu Mu, Takashi Kawashima, Davis V Bennett, Chao-Tsung Yang et al. doi:10.1038/nmeth.3040 See also: News and Views by Cunningham Guided visual exploration of genomic stratifications in cancer   pp884 - 885 Marc Streit, Alexander Lex, Samuel Gratzl, Christian Partl, Dieter Schmalstieg et al. doi:10.1038/nmeth.3088 Research Highlights Top Nanopores read long genomic DNA An ion-current map characteristic of four nucleotides traversing a protein nanopore allows resequencing of long DNA reads. Optical inhibition in red The red light-sensitive optogenetic inhibitor Jaws enables the modulation of neural activity deep inside the brain. A protein code to target RNA The protein-RNA specificity code of an RNA-binding protein can be used to target diverse transcripts in the cell for regulation. Unraveling the lncRNA mystery A method to study the domain architecture of long noncoding RNAs provides insights into their biological functions. Hitting the mark Genome-editing technologies generally stay on target, but researchers should remain vigilant for variants acquired during experimental manipulation. Methods in Brief Abnormalities during reprogramming | Following transcription in real time | Intracellular topology | Identifying genetic barriers to reprogramming Tools in Brief Watching auxin make its move | Pinpointing postsynaptic partners | Another hit to the gut microbiome | Myelination in arrays Methods JOBS of the week Assistant Professor in Biology University of Delaware Faculty Positions in Physical and Analytical Chemistry Ecole Polytechnique Fédérale de Lausanne (EPFL) Post-Doctoral Research Associate Georgia State University More Science jobs from Methods EVENT Can We Afford NOT to Monitor Priority Pollutants 12th November 2014 London, UK More science events from Commentaries Top Improved reproducibility by assuring confidence in measurements in biomedical research   pp895 - 898 Anne L Plant, Laurie E Locascio, Willie E May and Patrick D Gallagher doi:10.1038/nmeth.3076 'Irreproducibility' is symptomatic of a broader challenge in measurement in biomedical research. From the US National Institute of Standards and Technology (NIST) perspective of rigorous metrology, reproducibility is only one aspect of establishing confidence in measurements. Appropriate controls, reference materials, statistics and informatics are required for a robust measurement process. Research is required to establish these tools for biological measurements, which will lead to greater confidence in research results. A critique of methods for temperature imaging in single cells   pp899 - 901 Guillaume Baffou, Hervé Rigneault, Didier Marguet and Ludovic Jullien doi:10.1038/nmeth.3073 We argue that standard thermodynamic considerations and scaling laws show that a single cell cannot substantially raise its temperature by endogenous thermogenesis. This statement seriously questions the interpretations of recent work reporting temperature heterogeneities measured in single living cells. Technology Feature Top Structural biology: 'seeing' crystals the XFEL way   pp903 - 908 Vivien Marx doi:10.1038/nmeth.3070 X-ray free-electron lasers (XFELs) offer opportunities beyond classic X-ray crystallography, particularly for proteins that are difficult to crystallize. News and Views Top Analyzing neural data at huge scale   pp911 - 912 John P Cunningham doi:10.1038/nmeth.3071 A new distributed computing framework for data analysis enables neuroscientists to meet the computational demands of modern experimental technologies. See also: Correspondence by Vladimirov et al. | Article by Amat et al. | Article by Freeman et al. Brief Communications Top Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum   pp915 - 918 Jeffrey C Wagner, Randall J Platt, Stephen J Goldfless, Feng Zhang and Jacquin C Niles doi:10.1038/nmeth.3063 Single guide RNAs driven by a T7 promoter target Cas9 to two endogenous loci, leading to fast and efficient genome editing in the malaria parasite P. falciparum. High-resolution reconstruction of the beating zebrafish heart   pp919 - 922 Michaela Mickoleit, Benjamin Schmid, Michael Weber, Florian O Fahrbach, Sonja Hombach et al. doi:10.1038/nmeth.3037 A series of technical and analytical improvements to light sheet microscopy is described, permitting dynamic imaging of the beating zebrafish heart at cellular resolution. Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser   pp923 - 926 David Arnlund, Linda C Johansson, Cecilia Wickstrand, Anton Barty, Garth J Williams et al. doi:10.1038/nmeth.3067 A 'protein quake' is directly monitored on the picosecond timescale using the method of time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. High-resolution structure determination by continuous-rotation data collection in MicroED   pp927 - 930 Brent L Nannenga, Dan Shi, Andrew G W Leslie and Tamir Gonen doi:10.1038/nmeth.3043 High-resolution, three-dimensional protein structures can be solved using MicroED, an electron diffraction method that uses three-dimensional microcrystals. An improved MicroED data collection approach described here increases data quality and resolution and extends its broad applicability. Nanoscale high-content analysis using compositional heterogeneities of single proteoliposomes   pp931 - 934 Signe Mathiasen, Sune M Christensen, Juan José Fung, Søren G F Rasmussen, Jonathan F Fay et al. doi:10.1038/nmeth.3062 The compositional heterogeneity of proteoliposome reconstitution can skew the results of ensemble-average measurements of transmembrane protein structure and function. These compositional heterogeneities can be exploited, however, with a single-proteoliposome, high-content screening method. Phen-Gen: combining phenotype and genotype to analyze rare disorders   pp935 - 937 Asif Javed, Saloni Agrawal and Pauline C Ng doi:10.1038/nmeth.3046 To find causative mutations in rare disorders, the Phen-Gen software combines disease symptoms and sequencing data with prior knowledge about the gene. Epiviz: interactive visual analytics for functional genomics data   pp938 - 940 Florin Chelaru, Llewellyn Smith, Naomi Goldstein and Héctor Corrada Bravo doi:10.1038/nmeth.3038 Integration of genome visualization with Bioconductor-based analysis tools allows rapid and interactive analysis of genomes, transcriptomes and epigenomes. Advertisement BD LSRFortessa™ X-20 with ultraviolet laser  Expand your research capabilities by adding the ultraviolet channel to your multicolor flow cytometry studies. Special upgrade offers let you take advantage of a whole new spectrum of choice and productivity with a dedicated ultraviolet laser position and new ultraviolet excitable dyes. bdbiosciences.com/go/ultra   Articles Top Mapping brain activity at scale with cluster computing   pp941 - 950 Jeremy Freeman, Nikita Vladimirov, Takashi Kawashima, Yu Mu, Nicholas J Sofroniew et al. doi:10.1038/nmeth.3041 An open-source library of analytical tools for mapping large-scale patterns of brain activity using cluster computing finds structure in two-photon imaging data from mouse and whole-brain light-sheet functional imaging data from behaving larval zebrafish. Vladimirov et al., also in this issue, describes the light-sheet functional imaging system used here. See also: News and Views by Cunningham Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data   pp951 - 958 Fernando Amat, William Lemon, Daniel P Mossing, Katie McDole, Yinan Wan et al. doi:10.1038/nmeth.3036 This paper describes automated methods for the accurate segmentation and tracking of tens of thousands of nuclei in time-lapse imaging data of developing embryos. See also: News and Views by Cunningham RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)   pp959 - 965 Nathan A Siegfried, Steven Busan, Greggory M Rice, Julie A E Nelson and Kevin M Weeks doi:10.1038/nmeth.3029 The combination of selective 2'-hydroxyl acylation of RNA with high-throughput sequencing of the transcribed cDNA allows identification of chemically modified sites as mutations in the sequence that then yield highly accurate secondary-structure models of the RNA. Isolation of rare recombinants without using selectable markers for one-step seamless BAC mutagenesis   pp966 - 970 George T Lyozin, Paul C Bressloff, Amit Kumar, Yasuhiro Kosaka, Bradley L Demarest et al. doi:10.1038/nmeth.3030 Application of the founder principle from population genetics to variant selection after recombineering allows the isolation of rare unselected recombinants. Addendum Top Addendum: Independent optical excitation of distinct neural populations   p972 Nathan C Klapoetke, Yasunobu Murata, Sung Soo Kim, Stefan R Pulver, Amanda Birdsey-Benson et al. doi:10.1038/nmeth0914-972 Corrigenda Top Corrigendum: Fluorophore localization algorithms for super-resolution microscopy   p971 Alex Small and Shane Stahlheber doi:10.1038/nmeth0914-971a Corrigendum: Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study   p971 Pieter Mestdagh, Nicole Hartmann, Lukas Baeriswyl, Ditte Andreasen, Nathalie Bernard et al. doi:10.1038/nmeth0914-971b Corrigendum: A holidic medium for Drosophila melanogaster   p971 Matthew D W Piper, Eric Blanc, Ricardo Leitão-Goncalves, Mingyao Yang, Xiaoli He et al. doi:10.1038/nmeth0914-971c Corrigendum: Independent optical excitation of distinct neural populations   p971 Nathan C Klapoetke, Yasunobu Murata, Sung Soo Kim, Stefan R Pulver, Amanda Birdsey-Benson et al. doi:10.1038/nmeth0914-971d Application Notes Top Chromatrap® 96: a new solid-state platform for high-throughput ChIP    Amy L Beynon, Lindsay J Parkes, Matthew L Turner, Steve Knight, Steve Conlan et al. One solution for cloning and mutagenesis: In-Fusion® HD Cloning Plus    Malathi Raman and Karen Martin Top Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast on: Targeting the untargeted in translational research Thursday September 11, 2014 Session 1: Europe and the Middle East 2PM BST, 3pm CEST, 5PM GST Session 2: USA 9AM PDT, 11AM CDT, 12PM EDT  Register for the webcast and live Q and A session Sponsored by:Agilent   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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